Usage

There are two ways to use RNA-Pareto. The first is an interactive
graphical user interface written in Java. The second is a command-line
tool, which allows to process the calculated solutions further in own
programs.

Graphical User Interface (GUI)

To start the GUI, click on "RNAPareto.sh" (on Linux), "RNAPareto.exe"
(on Windows) or on the RNAPareto app (on Mac), or just type "java -jar
RNAPareto.jar" on the command line. An RNA database in FASTA format can
then be loaded. After choosing two RNA sequence from this databse,
click "Start" to begin the calculation of the Pareto-set of solutions.
Using the scatter plot of solutions in the center of the window, choose
interesting solutions, which are then displayed.

Output of the command-line tool

There is also a standalone command-line tool, which is called
"rna-pareto" (on Linux or Mac) or "rna-pareto.exe" (on Windows). This
program outputs all Pareto-optimal solutions, each consisting of 5
lines:

three numbers x y z, where

x is the sequence score

y is the structure score

z = A+B

line one of the alignment, containing sequence A

line two of the alignment, containing sequence B

the consensus secondary structure

a blank line

Compile from source

The C++ part can be compiled from source. Therefore, the Vienna RNA
library has to be present, as well as some Java JDK. There are three
Makefiles, because they differ for Linux, Mac and Windows. You may have
to change some paths in the makefiles to get all to compile. The Java
part was developed using Eclipse IDE. Therefore it should be possible to
import the project into eclipse. To get it to work, the appropriate JNI
library has to be present in the working directory.

Troubleshoting on Mac OS X 10.8 Mountain Lion

On some recent versions of Mac OS X, an error message appears
("RNAPareto is damaged and can't be opened."). This happens because
Gatekeeper disallows starting unsigned apps downloaded from the internet
by default. To run RNAPareto, apply the following steps: